fixed a few typos

eh... a missing fix
This commit is contained in:
Heng Li 2017-09-16 22:52:26 -04:00
parent 1d90742b35
commit 8cdaae0935
1 changed files with 6 additions and 6 deletions

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@ -9,7 +9,7 @@ minimap2 and provides a convenient interface to calling minimap2 in Python.
Installation
------------
The minimap2 model can be installed directly with:
The minimap2 module can be installed directly with:
.. code:: shell
@ -31,13 +31,13 @@ The following Python program shows the key functionality of this module:
.. code:: python
import minimap2 as mm
a = mm.Aligner("test/MT-human.fa")
a = mm.Aligner("test/MT-human.fa") # load or build index
if not a: raise Exception("ERROR: failed to load/build index")
for hit in a.map("GGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTTAATTTCTGT"):
print("{}\t{}\t{}\t{}".format(hit.ctg, hit.r_st, hit.r_en, hit.cigar_str))
It builds an index from the specified sequence file (or loads an index if a
pre-built index is supplied), aligns a sequence against it, traverses each hit
pre-built index is specified), aligns a sequence against it, traverses each hit
and prints them out.
APIs
@ -81,9 +81,9 @@ Arguments:
.. code:: python
map(query_seq)
map(seq)
This methods maps :code:`query_seq` against the index. It *yields* a generator,
This method maps :code:`seq` against the index. It *yields* a generator,
generating a series of :code:`Alignment` objects.
Class minimap2.Alignment
@ -118,7 +118,7 @@ This class has the following properties:
* **cigar**: CIGAR returned as an array of shape :code:`(n_cigar,2)`. The two
numbers give the length and the operator of each CIGAR operation.
An Alignment object can be converted to a string in the following format:
An :code:`Alignment` object can be converted to a string in the following format:
::